Calcium in PDB 3hjr: Crystal Structure of Serine Protease of Aeromonas Sobria

The structure of Crystal Structure of Serine Protease of Aeromonas Sobria, PDB code: 3hjr was solved by H.Utsunomiya, H.Tsuge, H.Kobayashi, K.Okamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.02 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.820, 112.056, 51.881, 90.00, 110.75, 90.00
R / Rfree (%)	16.8 / 20.2

The binding sites of Calcium atom in the Crystal Structure of Serine Protease of Aeromonas Sobria (pdb code 3hjr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Serine Protease of Aeromonas Sobria, PDB code: 3hjr:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Serine Protease of Aeromonas Sobria


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Serine Protease of Aeromonas Sobria within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:22.9 occ:1.00 O A:VAL126 2.3 6.0 1.0 O A:THR132 2.3 8.1 1.0 OD2 A:ASP87 2.4 8.3 1.0 O A:ILE130 2.4 10.0 1.0 OD1 A:ASN29 2.4 10.2 1.0 OD1 A:ASN128 2.4 7.4 1.0 OD1 A:ASP87 2.5 8.9 1.0 CG A:ASP87 2.8 8.4 1.0 CG A:ASN29 3.5 7.3 1.0 CG A:ASN128 3.5 7.7 1.0 C A:VAL126 3.5 8.0 1.0 C A:THR132 3.5 8.6 1.0 C A:ILE130 3.6 9.8 1.0 N A:THR132 3.8 8.4 1.0 ND2 A:ASN128 4.0 5.8 1.0 N A:ASN128 4.0 7.8 1.0 C A:GLY131 4.0 7.9 1.0 CB A:ASN29 4.1 6.7 1.0 N A:VAL126 4.2 7.2 1.0 CA A:THR132 4.3 7.9 1.0 CG1 A:ILE130 4.3 8.7 1.0 CB A:ASP87 4.3 8.2 1.0 CA A:VAL126 4.4 7.5 1.0 N A:ILE130 4.4 10.0 1.0 CA A:GLY131 4.4 8.7 1.0 N A:GLY131 4.4 8.9 1.0 N A:ASP127 4.5 7.9 1.0 CA A:ILE130 4.5 9.4 1.0 O A:GLY131 4.5 8.2 1.0 ND2 A:ASN29 4.5 8.5 1.0 N A:LYS133 4.6 9.6 1.0 CA A:ASP127 4.6 8.0 1.0 CB A:ASN128 4.7 7.4 1.0 CB A:VAL126 4.7 7.3 1.0 CA A:ASN128 4.7 7.1 1.0 O A:ASN128 4.7 6.8 1.0 C A:ASN128 4.7 8.3 1.0 C A:ASP127 4.7 7.6 1.0 C A:ALA125 4.8 8.4 1.0 CA A:LYS133 4.8 9.6 1.0 CA A:ASN29 4.9 6.5 1.0 CB A:ALA125 4.9 9.1 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Serine Protease of Aeromonas Sobria


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Serine Protease of Aeromonas Sobria within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:33.2 occ:1.00 OD1 A:ASP454 2.4 8.0 1.0 O A:ALA555 2.4 6.7 1.0 OD1 A:ASN579 2.4 10.5 1.0 OD1 A:ASP553 2.5 8.2 1.0 OD1 A:ASP488 2.5 6.0 1.0 OD1 A:ASN578 2.6 7.8 1.0 OD2 A:ASP553 2.8 12.7 1.0 CG A:ASP553 3.1 6.6 1.0 CG A:ASP488 3.4 5.5 1.0 CG A:ASN579 3.5 12.0 1.0 C A:ALA555 3.6 6.5 1.0 CG A:ASP454 3.6 15.5 1.0 O A:ASP454 3.6 19.6 1.0 CG A:ASN578 3.6 8.0 1.0 CB A:ASP488 3.7 6.0 1.0 ND2 A:ASN578 4.1 10.7 1.0 ND2 A:ASN579 4.1 10.6 1.0 NH1 A:ARG485 4.2 3.8 1.0 CA A:ASN556 4.2 6.6 1.0 OD2 A:ASP454 4.2 17.6 1.0 NE2 A:HIS483 4.2 5.3 1.0 CE1 A:HIS483 4.2 6.6 1.0 O A:HOH1235 4.3 46.0 1.0 OD2 A:ASP488 4.3 5.0 1.0 N A:ASN556 4.3 5.9 1.0 C A:ASP454 4.4 16.0 1.0 N A:ASN579 4.5 9.2 1.0 CB A:ASP553 4.6 5.4 1.0 CA A:ASP454 4.6 15.8 1.0 CB A:ASN556 4.6 7.1 1.0 NE A:ARG485 4.6 5.4 1.0 N A:ALA555 4.6 6.4 1.0 CA A:ALA555 4.6 6.0 1.0 CB A:ASP454 4.7 15.7 1.0 CB A:ASN579 4.8 10.9 1.0 CZ A:ARG485 4.9 6.0 1.0 CB A:ASN578 4.9 8.8 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Serine Protease of Aeromonas Sobria


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Serine Protease of Aeromonas Sobria within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:27.8 occ:1.00 O A:MET303 2.3 10.6 1.0 O A:CYS326 2.3 10.2 1.0 O A:GLY300 2.3 10.1 1.0 O A:LEU298 2.4 7.6 1.0 O A:ASN306 2.4 9.2 1.0 OD1 A:ASP297 2.5 6.6 1.0 C A:MET303 3.5 11.0 1.0 C A:GLY300 3.5 9.9 1.0 C A:CYS326 3.5 10.8 1.0 CG A:ASP297 3.5 9.5 1.0 C A:LEU298 3.6 8.2 1.0 C A:ASN306 3.6 9.7 1.0 CB A:CYS326 3.7 11.1 1.0 N A:GLY300 3.9 9.3 1.0 C A:PRO299 4.1 9.1 1.0 CB A:ASP297 4.1 8.6 1.0 CA A:GLY304 4.2 10.2 1.0 CA A:CYS326 4.3 11.4 1.0 N A:GLY304 4.3 10.0 1.0 CA A:GLY300 4.3 10.2 1.0 CB A:ASN306 4.3 9.9 1.0 CA A:ASN306 4.3 10.2 1.0 N A:ASN306 4.4 9.9 1.0 O A:PRO299 4.5 8.8 1.0 N A:LEU298 4.5 9.4 1.0 CA A:PRO299 4.5 8.6 1.0 N A:PRO299 4.5 8.8 1.0 CA A:MET303 4.5 11.2 1.0 CA A:LEU298 4.5 8.8 1.0 N A:CYS301 4.5 10.8 1.0 OD2 A:ASP297 4.5 14.2 1.0 N A:MET303 4.5 11.6 1.0 N A:ASP327 4.6 10.4 1.0 N A:ARG307 4.7 10.2 1.0 CA A:CYS301 4.7 10.6 1.0 O A:SER325 4.7 12.5 1.0 CB A:LEU298 4.7 8.7 1.0 C A:GLY304 4.7 10.1 1.0 C A:ASP297 4.8 8.8 1.0 CB A:MET303 4.8 11.7 1.0 CA A:ASP327 4.8 10.5 1.0 CB A:ARG307 4.8 10.3 1.0 CG A:ASN306 4.9 9.0 1.0 CA A:ARG307 5.0 10.4 1.0

H.Kobayashi, H.Utsunomiya, H.Yamanaka, Y.Sei, N.Katunuma, K.Okamoto, H.Tsuge. Structural Basis For the Kexin-Like Serine Protease From Aeromonas Sobria As A Sepsis-Causing Factor J.Biol.Chem. V. 284 27655 2009.
ISSN: ISSN 0021-9258
PubMed: 19654332
DOI: 10.1074/JBC.M109.006114